Gliomas are the most common primary brain tumors and occur at an incidence of almost 12 per 100,000 people (Landis S H, Murray T, Bolden S and Wingo P A. (1999). Cancer J. Clin., 49, 8-31). Diffuse astrocytoma may be classified (as per WHO classification) as low-grade diffuse (DA; Grade II), anaplastic (AA; Grade III) and glioblastoma (Grade IV; GBM), in the order of increasing, malignancy (Mischel P S and Vinters H V. (2001). (Ed. Liau, L.M.e.a.) Humana Press; Totowa, N.J., pp. 3-45). Currently, these classifications are based on the observed histopathological characteristics of the tumor, which are sometimes subjective and inconsistent. GBM constitutes more than 80% of malignant gliomas and patients with GBM have a median survival of less than one year. Current treatments, including surgery, radiation therapy, and chemotherapy, unfortunately have not changed the natural history of these incurable neoplasms; and the prognosis of patients with GBMs, has not improved significantly in the past 30 years (Davis F, Freels. S, Grutsch J, Barlas S and Brem S. (1998). J. Neurosurg., 88, 1-10). To find new diagnostic and therapeutic strategies, a better understanding of the biological pathway(s) leading to glial tumorigenesis is warranted.
Astrocytoma development is known to involve accumulation of a series of genetic alterations (Nagane M, Su Huang H J and Cavenee W K. (1997). Curr. Opin. Oncol., 9, 215-222) similar to other cancers. Identification of many of the genes involved in astrocytoma development, using standard molecular approaches, has helped to understand the process of astrocytoma genesis and progression (Louis D N and Gusella J F. (1995). Trends in Genetics, 11, 412-415). Frequent amplification of epidermal growth factor receptor (EGFR) (Hill J R, Kuriyama N, Kuriyama H and Israel M A. (1999). Arch. Neurol., 56, 439-441; Brock C S and Bower M. (1997). Medical Oncology, 14, 103-120), platelet derived growth factor receptor (PDGFR) (Hermanson M K, Funa M, Hartman L, Claesson-Welsh C H, Heldin B, Westermark and Nistér M. (1992). Cancer Res., 52, 3213-3219; Hermanson M, Funa K, Koopman J, Maintz D, Waha A, Westermark, B, Heldin, C H, Wiestler, O D, Louis D N, von Deimling A and Nistér M. (1996). Cancer Res, 56, 164-171; Maxwell M, Naber S P, Wolfe H J, Galanopoulos T, Hedley-Whyte E T, Black P and Antoniades N. (1990). J. Clin. Invest., 85, 131-40; Westermark B, Heldin C H, and Nistér M. (1995). Glia, 15, 257-263; Fleming T P, Saxena A, Clark W C, Robertson J T, Oldfield E H, Aaronson S A and Ali I U. (1992). Cancer Res., 52, 4550-4553), amplification of chromosome 12q region, which carries the cdk4 gene (Nagane M, Su Huang H J and Cavenee W K. (1997). Curr. Opin. Oncol., 9, 215-222; Hill J R, Kuriyama N, Kuriyama H and Israel M A. (1999). Arch. Neural., 56, 439-441) and alterations in chromosomes 1p, 9p, 10, 17p, 19q, and 22q have frequently been found in these tumors. In addition, mutations in the tumor suppressor gene p53 were found to be associated with chromosome 17p alterations in low grade and progressive astrocytoma (Maher E A, Furnari F B, Bachoo R M, Rowitch D H, Louis D N, Cavenee W K and DePinho R A. (2001). Genes Dev., 15, 1311-1333; Phatak P, Kalai Selvi S, Divya T, Hegde A S, Hegde S and Somasundaram K. (2002). J. Bioscience, 27, 673-686). Inactivation of the cdk inhibitor p16 INK4a residing in chromosome 9p, is very common in sporadic astrocytoma, occurring in 50-70% of high-grade gliomas and 90% of GBM cell lines (James C D, He J, Carlbom E, Nordenskjold M, Cavenee W K and Collins V P. (1991). Cancer Res., 51, 1684-1688; Olopade O I, Jenkins R B, Ransom D T, Malik K, Pomykala H, Nobori T, Cowan J M, Rowley J D and Diaz M O. (1992). Cancer Res., 52, 2523-2529). LOH in chromosome 10 is one of the most frequent alterations in GBM and is accompanied by the loss of PTEN/MMAC gene (Hill J R, Kuriyama N, Kuriyama H and Israel M A. (1999). Arch. Neurol., 56, 439-441).
Despite all this information about astrocytoma, our understanding of astrocytoma development is not sufficient enough to improve prognosis for GBM patients. A more global, systematic understanding of expression patterns of various genes and their downstream gene products in astrocytoma will hopefully provide new diagnostic and therapeutic targets. Towards this, a number of studies have reported the gene expression profile of astrocytoma (Liau L M, Lallone R L, Seitz R S, Buznikov A, Gregg J P, Kornblum H I, Nelson S F and Bronstein J M. (2000). Cancer Res., 60, 1353-1360; Sallinen S L, Sallinen P K, Haapasalo M K, Helin H J, Helen P T, Schraml P, Kallioniemi O P and Kononen J. (2000). Cancer Res., 60, 6617-6622; Rickman D S, Bobek M P, Misek D E, Kuick R, Blaivas M, Kurnit D M, Taylor J and Hanash S M. (2001). Cancer Res., 61, 6885-6891; Ljubimova J Y, Lakhter A J, Loksh A, Yong W H, Riedinger M S, Miner J H, Sorokin L M, Ljubimova A V and Black K L. (2001). Cancer Res., 61, 5601-5610; Watson M A, Perry A, Budhjara V, Hicks C, Shannon W D and Rich K M. (2001). Cancer Res., 61, 1825-1829; Tanwar M K, Gilbert M R and Holland E C. (2002). Cancer Res., 62, 4364-4368; Fathallah-Shaykh H M, Rigen M, Zhao L J, Bansal K, He B, Engelhard H H, Cerullo L, Von Roenn K, Byrne R, Munoz L, Rosseau G L, Glick R, Lichtor T and DiSavino E. (2002). Oncogene, 21, 7164-7174; Nutt C L, Math D R, Betensky R A, Tamayo P, Cairncross J G, Ladd C, Pohl U, Hartmann C, McLaughlin M E, Batchelor T T, Black P M, von Deimling A, Pomeroy S L, Golub T R and Louis D N. (2003). Cancer Res., 63, 1602-1607; Wang. H, Wang H, Shen W, Huang H, Hu L, Ramdas L, Zhou Y, Liao W S L, Fuller G N and Zhang. W. (2003). Cancer Res., 63, 4315-4321; Godard S, Getz G, Delorenzi M, Farmer P, Kobayashi H, Desbaillets I, Michimasa N, Diserens A C, Hamou M F, Dietrich P Y, Regli L, Janzer R C, Bucher P, Stupp R, de Tribolet N, Domany E and Hegi M E. (2003). Cancer Res., 63, 6613-6625).
It is also desirable to be able to target specific therapeutic modalities to pathogenically distinct tumor types to maximize efficacy and minimize toxicity to the patient. (Golub T R, Slonim D K, Tamayo P, Huard C, Gaasenbeek M, Mesirov J P, Coller H, Loh M L, Downing J R, Caligiuri M A, Bloomfield C D, Lander E S. (1999) Science 286, 531-37; Kleihues Kudoh K, Ramanna M, Ravatn R, Elkahloun A G, Bittner M L, Meltzer P S, Trent J M, Dalton W S, Chin K V. (2000) Cancer Res. 60(15), 4161-66). Previously, cancer classification has been based primarily on the morphological appearance of tumor cells. But this has serious limitations, because tumors with similar histopathological appearance can follow significantly different clinical courses and show different responses to therapy. For example, based on histopathological appearance, astrocytoma grade IV cannot consistently be distinguished from astrocytoma grade III.
Immunophenotyping for brain tumors has defined and refined diagnosis, e.g., distinguishing oligoastrocytoma from astrocytomas, and high-grade from low-grade astrocytomas. However, differential protein expression (GFAP, vimentin, synaptophysin, nestin) has not helped to improve therapeutic approaches. Prediction of transitions from low- to high-grade astrocytomas is difficult to make with currently available markers (De Girolami U, Cotran R C, Kumar V, Robbins S L. (1994) Pathologic basis of disease, 5th ed., W. B. Saunders Co., 1295-1357).
Zhang, J., Madden, T. L., (1997) Genome Res. 7(6), 649-56 (US Patent 20040053277) have identified a number of gene sets whose expression can accurately classify a glioma as glioblastoma (GBM), anaplastic astrocytoma (AA), anaplastic oligodendroglioma (AO) or oligodendroglioma (OL). Microarray gene expression profiling of glioma allows simultaneous analysis of thousands of genes and is likely to identify molecular markers associated with tumor grade, progression and survival. Through cDNA microarray experiments, we have identified genes which are differentially expressed between glioblastomas and lower-grade astrocytomas (grade II and grade III). Therefore, it is a desideratum to be able to diagnose the presence of astrocytoma and particularly its most malignant type i.e., glioblastoma and thus to be able to administer appropriate treatment. These and other benefits are provided by the present invention.